Position-specific modifications of histones provide epigenetic control of gene expression and silencing in eukaryotes (Nightingale et al., Curr Opin Genet Dev 16, 125-36 (2006); Fischle et al., Curr Opin Cell Biol 15, 172-83 (2003)). Such modifications include acetylation, methylation, phosphorylation and ubiquitination (Id.). Viruses recruit chromatin-associated transcriptional proteins for their genome maintenance and replication. For instance, the papillomavirus E2 protein binds Brd4 to tether the viral genome to mitotic chromosomes to ensure persistence of viral episomes in viral infected cells (You et al., Cell 117, 349-60 (2004); Wu et al., Genes Dev 20, 2383-96 (2006)). The adenovirus E1A protein interacts with the retinoblastoma protein p130 to disrupt a network of protein interactions required for silencing of E2F-responsive genes in quiescent cells (Ghosh et al., Mol Cell 12, 255-60 (2003)). Moreover, the trans-activator Tat from human immunodeficiency virus recruits the histone acetyltransferases p300/CBP (CREB binding protein) and PCAF (p300/CBP associated factor) for lysine acetylation of a nucleosome, a remodeling step required for transcriptional activation and replication of the integrated provirus (Mujtaba et al., Mol Cell 9, 575-86 (2002); Don et al., EMBO J 21, 2715-23 (2002)). Despite the indirect virus/host protein recruitment mechanisms to reconfigure chromatin structure for viral transcription, no viral enzymes have been reported that directly modify histones and modulate host gene transcription. Histone lysine methylation, except for H3-K79, is catalyzed by a family of SET domain proteins first identified in Drosophila proteins: Suppressor of variegation, Enhancer of zeste (E(z)) and Trithorax. (Bannister et al., Cell 109, 801-6 (2002); Lachner et al., J Cell Sci 116, 2117-24 (2003)). Position- and state-specific histone lysine methylation by SET domain proteins in a specific biological context specifies unique functional consequences (Bannister et al. and Lachner et al.). For instance, during cell proliferation, H3-K4 di-methylation by Set1 correlates with basal transcription, whereas H3-K4 tri-methylation occurs at fully activated promoters (Sims et al., Genes Dev 20, 2779-86 (2006); Wysocka et al., Nature 442, 86-90 (2006); Bernstein et al., Proc Natl Acad Sci USA 99, 8695-700 (2002)). Regional H3-K9 tri-methylation by Suv39h at transcriptionally inert chromatin domains is a hallmark of constitutive hetero-chromatin (Peters et al., Nat Genet 30, 77-80 (2002)). During cell differentiation, extended H3-K27 di- and tri-methylation by the Drosophila Polycomb group (PcG) Esc-E(z) complex or the mammalian counterpart Eed-Ezh2 complex are linked to Hox gene silencing, X-chromosome inactivation, germline development and stem cell pluripotency, as well as cancer (Czermin, B. et al. Cell 111, 185-196 (2002); Muller, J. et al., Cell 111, 197-208 (2002); Cao et al. Science 298, 1039-1043 (2002); Kuzmichev et al., Genes Dev 16, 2893-905 (2002); Plath et al. Science 300, 131-5 (2003); Boggs et al., Nat Genet 30, 73-6 (2002); Bernstein et al. Cell 125, 315-26 (2006); Boyer et al., Nature 441, 349-53 (2006); Lee et al. Cell 125, 301-13 (2006); Cao & Zhang, Curr Opin Genet Dev 14, 155-64 (2004)).
The high degree of modification complexity and coding potential of histone lysine methylation in epigenetic control may explain the existence of an unusually large family of SET domain proteins with more than 700 members (Schultz et al., Proc. Natl. Acad. Sci. U.S.A. 95, 5857-5864 (1998)). Notably, within this extensive family is a small subclass of SET domain proteins encoded by viruses and bacteria of which little is known about their cellular functions. One of these viral proteins is the SET domain protein (vSET) encoded by Paramecium bursaria chlorella virus 1 (PBCV-1) which specifically methylates Lys27 in histone 3, a modification implicated in gene silencing (Manzur et al., Nat Struct Biol., 10:187-196). PBCV-1 is the prototype of a family of large, icosahedral, double-stranded DNA—containing viruses that are known to replicate in certain unicellular, eukaryotic chlorella-like green algae, particularly zoochlorellae (Van Etten et al., Annu. Rev. Microbiol. 53, 447-494 (1999)). DNA sequence analysis of PBCV-1 reveals that this giant virus contains a large 330 kb genome of 376 protein-encoding genes (Li et al. Virology 237, 360-377 (1997)). The SET domain-containing PBCV-1 protein consists of 119 amino acids and represents the smallest known SET domain—containing protein in the SET domain family, although vSET lacks the cysteine-rich pre-SET and post-SET motifs flanking the conserved core SET domain. These pre-SET and post-SET motifs are required for histone methyltransferase activity in various SET domain proteins including human SUV39H1 (Rea et al. Nature 406, 593-599 (2000)). The presence of SET domain-like proteins in viruses raises questions about whether such proteins have histone modifying activities, and if so, what are the cellular consequences when these proteins are expressed in vivo (Qian & Zhou, Cell Mol Life Sci 63, 2755-63 (2006); Manzur et al., FEBS Lett 579, 3859-65 (2005); Alvarez-Venegas et al., Mol Biol Evol 24, 482-97 (2007)).